Interpretive Summary: Rhizobial bacteria form nodules on the roots of soybean plants. The nodules are specialized structures where atmospheric nitrogen is fixed by the bacterium, which in turn, is utilized by the soybean plants for growth and development. This process is termed biological nitrogen fixation and it enables soybean plants to grow in nitrogen-poor soils. Farmers apply commercial bacterial inoculums to boost nitrogen fixation. However, indigenous bacteria are very competitive and exclude the commercial inoculums from forming nodules on soybean roots. We have identified and characterized a gene that is important for competitiveness of Rhizobium to nodulate soybean. This information will enable manipulation of biological nitrogen fixation so that farmers can confidently apply commercial inoculums to increase the yield of soybean.

Technical Abstract:
Inositol derivative compounds provide a nutrient source for soil bacteria that possess the ability to degrade such compounds. Rhizobium strains that are capable of utilizing certain inositol derivatives are better colonizers of their host plants. We cloned and determined the nucleotide sequence of the myo-inositol dehydrogenase gene (idhA) of Sinorhizobium fredii USDA191, ,the first enzyme responsible for inositol catabolism. Inactivation of idhA by insertion of a kanamycin cassette in the coding region eliminated the ability of S. fredii USDA191 to grow on myo-inositol as a sole carbon source. Northern blot analysis and idhA-lacZ fusion expression studies indicate that idhA is inducible by myo-inositol. Southern blot analysis employing DNA from sym-plasmid-cured derivatives of S. fredii USDA192, USDA205 and Rhizobium strain NGR234 revealed the idhA was located on the chromosome. Although several diverse groups of rhizobia had idhA-similar sequences, they were not detected in three species of Bradyrhizobium, the traditional symbionts of soybeans. Sinorhizobium fredii USDA191 idhA mutant was drastically affected in its ability to reduce nitrogen and revealed developmental abnormalities in nodule ultrastructure. Electron microscopic observation of thin sections of soybean nodules initiated by the idhA mutant revealed deteriorating bacteroids inside the nodules. The number of bacteria recovered from such nodules was about three-fold lower than the number isolated from nodules initiated by S. fredii USDA191. The idhA mutant was also severely affected in its ability to compete with the wild- type strain to nodulate soybean. Under competitive conditions, nodules induced on soybean roots were predominantly occupied by the parent strain, even when the idhA mutant was applied at a 10-fold numerical advantage.